Functional Enrichment Analysis | Tool: gprofileR.

net_dir = "/pastel/projects/speakeasy_dlpfc/SpeakEasy_singlenuclei/2nd_pass/snakemake-sn/results/"

macro_type = params$cell_type #macro_structure. It can be cell_type, metabolites, region of the brain. 
message(paste0("Cluster: ", macro_type))
## Cluster: ast

Enrichment Level 03

We removed the clusters with < 30 nodes for downstream analysis.

modules_file = read.table(paste0(net_dir, macro_type, "/geneBycluster.txt"), header = T)
modules_file = modules_file[, c("gene_name", "cluster_lv3")]
modules_file$module_clusters = paste0("m", modules_file$cluster_lv3)
modules_file$cluster_lv3 = NULL
colnames(modules_file) = c("symbol", "module_clusters") #only the sn was with gene_name instead of symbol

modules_size = as.data.frame(table(modules_file$module_clusters))
colnames(modules_size) = c("module", "n_nodes")
createDT(modules_size)

Module enrichment L3

Module m16

Module m10

Module m20

Module m24

Module m5

Module m4

Module m2

Module m18

Module m29

Module m17

Module m13

Module m6

Module m11

Module m1

Module m14

Module m12

Module m21

Module m3

Module m19

Module m15

Module m25

Module m23

Module m27

Module m28

Module m7

Module m26

Session info

sessionInfo()

R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Stream 8

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] DT_0.20 plotly_4.10.0 knitr_1.37 gprofiler2_0.2.1 ggeasy_0.1.3 readxl_1.3.1 kableExtra_1.3.4 R.matlab_3.6.2 forcats_0.5.1 stringr_1.4.0
[11] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 tidyverse_1.3.1 limma_3.50.1 ggfortify_0.4.14 ggplot2_3.3.5

loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.5.2 lubridate_1.8.0 webshot_0.5.2 RColorBrewer_1.1-2 httr_1.4.2 tools_4.1.2 backports_1.4.1 bslib_0.3.1
[10] utf8_1.2.2 R6_2.5.1 vipor_0.4.5 DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3 withr_2.4.3 tidyselect_1.1.2 gridExtra_2.3
[19] compiler_4.1.2 cli_3.2.0 rvest_1.0.2 xml2_1.3.3 sass_0.4.0 scales_1.1.1 systemfonts_1.0.4 digest_0.6.29 rmarkdown_2.11
[28] svglite_2.1.0 R.utils_2.11.0 pkgconfig_2.0.3 htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.1 rstudioapi_0.13
[37] shiny_1.7.1 jquerylib_0.1.4 generics_0.1.2 jsonlite_1.7.3 crosstalk_1.2.0 R.oo_1.24.0 RCurl_1.98-1.6 magrittr_2.0.2 Rcpp_1.0.8
[46] ggbeeswarm_0.6.0 munsell_0.5.0 fansi_1.0.2 lifecycle_1.0.1 R.methodsS3_1.8.1 stringi_1.7.6 yaml_2.3.5 grid_4.1.2 promises_1.2.0.1
[55] crayon_1.5.0 haven_2.4.3 hms_1.1.1 pillar_1.7.0 reprex_2.0.1 glue_1.6.1 evaluate_0.15 data.table_1.14.2 modelr_0.1.8
[64] httpuv_1.6.5 vctrs_0.3.8 tzdb_0.2.0 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.29 mime_0.12 xtable_1.8-4
[73] broom_0.7.12 later_1.3.0 viridisLite_0.4.0 pheatmap_1.0.12 beeswarm_0.4.0 ellipsis_0.3.2